I hear the word “pettoro-su” (pet loss) surprisingly often these days, and it seems a lot of funeral parlors and graveyards are springing up to help bereaved owners put their loved ones to rest. One of the biggest companies is called Petto Ceremoni- Makoto (Sincere Pet Ceremonies), and it offers a wide range of pet funerals and cremations.
If you want to give your pet a sendoff, they have contracts with Buddhist temples to perform ceremonies.
After the funeral, you can have your pet’s ashes stores in a charnel house. According to their brochure, “The Shou Kannon watches over the charnel house. It’s said to be a Bodhisattva with great compassion, so you’ll be able to feel confident that your beloved pet’s soul is resting in peace through it’s enfolding kindness.” The urn storage service is free the first year, and costs 5,000 yen per year after that.
Here’s an article with more information about pet funerals: http://www.asiaone.com/News/Latest%2BNews/Asia/Story/A1Story20090702-152168.html